<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0101</schemaVersion>

<documentType>4</documentType><periodOfReport>2003-05-07</periodOfReport>
<issuer><issuerCik>0000874015</issuerCik>
        <issuerName>ISIS PHARMACEUTICALS INC</issuerName>
<issuerTradingSymbol>ISIS</issuerTradingSymbol></issuer><reportingOwner><reportingOwnerId><rptOwnerCik>0000897667</rptOwnerCik>
            <rptOwnerName>CROOKE STANLEY T</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>  </rptOwnerStreet1>
            <rptOwnerStreet2>  </rptOwnerStreet2>
            <rptOwnerCity>  </rptOwnerCity>
            <rptOwnerState>  </rptOwnerState>
            <rptOwnerZipCode>  </rptOwnerZipCode>
        </reportingOwnerAddress>
<reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>1</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther><officerTitle>Chairman, President, CEO</officerTitle></reportingOwnerRelationship></reportingOwner><derivativeSecurity><securityTitle><value>Employee Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>5.25</value></conversionOrExercisePrice><transactionDate><value>2003-05-07</value></transactionDate><deemedExecutionDate><value>2003-05-07</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>6250</value></transactionShares><transactionValue><value>5.25</value></transactionValue><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2007-05-07</value><footnoteId id="F1"/></exerciseDate><expirationDate><value>2013-05-06</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>6250</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>6250</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>By wife</value></natureOfOwnership></ownershipNature></derivativeSecurity><footnotes><footnote id="F1">Due to her part-time status, only 18.75% of the shares, 1,172 shares, subject to the option will vest and become exercisable on 5/7/2004.  Thereafter, 3,515 shares subject to the option vest and become exercisable in 36 equal monthly installments, at the rate of 1,172 shares per year, except the last year will vest 1,171 shares.  The option is exercisable as to 0 shares on 5/7/2003.  Dr. Crooke disclaims beneficial ownership of the shares of Common Stock owned and issuable upon exercise of options held by his wife.</footnote></footnotes><ownerSignature><signatureName>/s/Stanley T. Crooke</signatureName><signatureDate>2003-05-09</signatureDate></ownerSignature></ownershipDocument>

